To observe the effect of moxibustion on gastric mucosa injury index, the local structure of mitochondria and expression of type I collagen in acute gastric mucosal injury rabbits, and discuss the working mechanism of moxibustion on acute gastric mucosal injury from the perspective of gastric mucosal repair and energy metabolism of local acupoint. Methods: A group of New Zealand rabbits were randomly divided into normal group, model group, moxibustion group and western medicine group. As acute gastric mucosal injury model was successfully prepared, moxibustion group used ST36(Housanli) treatment, western medicine group used sucralfate gavage treatment. After the intervention, gastric mucosa and acupoint local tissue was reserved, using Guth method to observe index of gastric mucosal injury and transmission electron microscope to view local tissue mitochondrial morphology of ST36(Housanli). Also, immunohistochemistry was used to detect the expression of type I collagen. Results: Compared with the normal group, gastric mucosal injury index of rabbits in model group, western medicine group and herbs-partitioned moxibustion group were significantly increased (P<0.01). Cells in acupoint of model group appeared mitochondrial vacuolation, and expression of type I collagen was decreased (P<0.01). Besides, only a few mitochondria showed edema in moxibustion group and mitochondria decreased and mitochondrial cristae was not obvious in the western medicine group. Compared with the model group, gastric mucosal injury index decreased significantly (P<0.01), while the expression of type I collagen increased (P<0.01 or P<0.05) in moxibustion group and Western medicine group. Gastric mucosal injury index in moxibustion group was lower than that in western medicine group (P<0.01), thus type I collagen expression was higher than that in western medicine group, but the difference was not statistically significant (P>0.05). Conclusion: Herbs-partitioned moxibustion could improve mitochondrial morphology and increase the expression of collagen type I in acute gastric mucosal injury rabbits, which may be an effective approach to repair gastric mucosal injury.